- Current section: Introduction
- Learning outcomes
- 1 The three-dimensional nature of proteins
- 1.1 Introduction
- 1.2 The peptide bond and primary structure of proteins
- 1.3 Protein secondary structure
- 1.4 Protein tertiary structure
- 1.5 Quaternary structure
- 1.6 Fibrous proteins
- 1.7 Summary of Section 1
- 2 Assembling a functioning protein
- 3 Protein domains
- 4 Protein families and structural evolution
- 5 Dynamic proteins
- 6 Catalytic proteins
- 7 Studying protein function
- Next steps
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In this unit we explore how proteins are the 'doers' of the cell. They are huge in...
In this unit we explore how proteins are the 'doers' of the cell. They are huge in number and variety and diverse in structure and function, serving both the structural building blocks and the functional machinery of the cell. Just about every process in every cell requires specific proteins. The basic principles of protein structure and function which are reviewed in this unit are crucial to understanding how proteins perform their various roles.
By the end of this unit you should be able to:
- define and use each of the terms printed in bold in the text;
- describe the different levels of protein structure and their interdependence;
- explain how steric limitations determine secondary structure in polypeptides;
- describe, using examples, the relationship between protein structure and function;
- understand the significance of domains in protein function and how they have arisen;
- describe modifications of proteins and explain how these can affect the localisation, function or activity of the protein;
- give examples of how interaction of proteins with other molecules is critical to their function;
- describe experimental approaches to the study of protein–protein interactions;
- explain how site-directed mutagenesis can be used to study protein function;
- interpret and manipulate electronic three-dimensional models;
- devise simple experiments to analyse protein structure using SDS–PAGE and Western blotting techniques, and interpret the results of such experiments.
Proteins are the ‘doers’ of the cell. They are huge in number and variety and diverse in structure and function, serving as both the structural building blocks and the functional machinery of the cell. Just about every process in every cell requires specific proteins.
Let us begin by listing some of the basic cellular processes and the role that proteins play.
Chemical catalysis Enzymes, which are responsible for catalysing biological reactions, are the largest functional group of proteins. Whilst there are thousands of different enzymes, all catalysing different reactions, they do have some features in common and can often be identified as members of a particular family of enzymes.
Mechanical support Typically, support is provided by proteins, e.g. the cytoskeletal proteins inside the cell and the extracellular matrix proteins outside the cell.
Communication The signals within and between cells (e.g. cytokines) and the apparatus for recognising and interpreting or reacting to signals (receptors and transducers) are mainly proteins.
Adhesion Cell surface proteins mediate contact between cells and between a cell and the extracellular matrix (which is also made up of proteins).
Movement Proteins generate movement in a cell (motor proteins).
Defence Antibodies (immunoglobulins) are proteins that recognise specific targets (usually proteins themselves). This facility is critical for an immune response.
Transport Proteins are key molecules in the transport of substances both within a cell and to and from the cell.
Storage A number of proteins serve to store small molecules or ions; for example, ferritin binds iron and stores it in the liver.
You will come across many examples in this unit of proteins performing the functions outlined above, and the molecular basis for various cellular processes will be examined in some detail. The basic principles of protein structure and function, which are reviewed in this unit, are crucial to understanding how proteins perform their various roles.
The huge diversity in the functions of proteins is reflected in the specialisation of these molecules. As you will see in this unit, every protein optimally performs a particular job and the key to how it does so is its structure. The refinement of protein structure and optimisation of protein function are driven by evolutionary pressures. Mutations at the DNA level that result in a change in protein structure and function will persist if they enhance survival or are not detrimental to the organism.
Proteins come in as many different shapes and sizes (Figure 1) as they have functions. A broad distinction is made between globular proteins and fibrous proteins. Globular proteins are a particularly diverse group that includes enzymes, receptors and transport proteins, and are characterised by a roughly spherical compact shape. Fibrous proteins are elongated and rod-like (e.g. collagen, represented in (Figure 1) and often have a structural role. Most of the proteins discussed in this unit are globular proteins, which reflects both their number and the fact that they lend themselves to structural analysis by X-ray diffraction and NMR.
In this unit, we will consider aspects of the structure of proteins and illustrate how, through their interactions with other cellular components, they can function as dynamic molecular machines. We will begin by exploring the three-dimensional nature of proteins, reviewing some of their biochemistry and the biophysical rules that determine their structure and studying key structural elements that are common to many proteins. You will encounter these activities as you progress through the unit. The relationship between protein structure and function is explored using as examples a variety of different proteins, including enzymes, signalling proteins and transport proteins. All proteins bind other substances, often other proteins or organic molecules or inorganic ions. These interactions are integral to a protein's function and their specificity and affinity are critically determined by the protein's structure. This aspect is discussed at some length. The unit finishes with a consideration of some of the techniques employed in studying protein–protein interactions.
This unit is an adapted extract from the Open University course S377.